Wrappers

Wrapper functions for convenient access to the NBA

specimen_count()

Get the number of specimens matching a given condition

specimen_count_distinct_values()

Count the distinct number of values that exist for a given field

specimen_count_distinct_values_per_group()

Count the distinct number of field values that exist per the given field to group by

specimen_download_query()

Dynamic download service: Query for specimens and return result as a stream ...

specimen_dwca_get_data_set()

Download dataset as Darwin Core Archive File

specimen_dwca_get_data_set_names()

Retrieve the names of all available datasets

specimen_dwca_query()

Dynamic download service: Query for specimens and return result as Darwin Core Archive File

specimen_exists()

Returns whether or not a unitID for a specimen exists

specimen_find()

Find a specimen by id

specimen_find_by_ids()

Find specimens by ids

specimen_find_by_unit_id()

Find a specimen by unitID

specimen_get_distinct_values()

Get all different values that exist for a field

specimen_get_distinct_values_per_group()

Get all distinct values (and their document count) for the field given divided per distinct value of the field to group by

specimen_get_field_info()

Returns extended information for each field of a specimen document

specimen_get_ids_in_collection()

Retrieve all ids within a 'special collection' of specimens

specimen_get_named_collections()

Retrieve the names of all 'special collections' of specimens

specimen_get_paths()

Returns the full path of all fields within a document

specimen_get_setting()

Get the value of an NBA setting

specimen_get_settings()

List all publicly available configuration settings for the NBA

specimen_group_by_scientific_name()

Aggregates Taxon and Specimen documents according to their scientific names

specimen_is_operator_allowed()

Checks if a given operator is allowed for a given field

specimen_query()

Query for specimens

taxon_count()

Get the number of taxa matching a given condition

taxon_count_distinct_values()

Count the distinct number of values that exist for a given field

taxon_count_distinct_values_per_group()

Count the distinct number of field values that exist per the given field to group by

taxon_download_query()

Dynamic download service: Query for taxa and return result as a stream ...

taxon_dwca_get_data_set()

Download dataset as Darwin Core Archive File

taxon_dwca_get_data_set_names()

Retrieve the names of all available datasets

taxon_dwca_query()

Dynamic download service: Query for taxa and return result as Darwin Core Archive File

taxon_find()

Find a taxon by id

taxon_find_by_ids()

Find taxa by ids

taxon_get_distinct_values()

Get all different values that can be found for one field

taxon_get_distinct_values_per_group()

Get all distinct values (and their document count) for the field given divided per distinct value of the field to group by

taxon_get_field_info()

Returns extended information for each field of a specimen document

taxon_get_paths()

Returns the full path of all fields within a document

taxon_get_setting()

Get the value of an NBA setting

taxon_get_settings()

List all publicly available configuration settings for the NBA

taxon_group_by_scientific_name()

Aggregates Taxon and Specimen documents according to their scientific names

taxon_is_operator_allowed()

Checks if a given operator is allowed for a given field

taxon_query()

Query for taxa

multimedia_count()

Get the number of multimedia documents matching a given condition

multimedia_count_distinct_values()

Count the distinct number of values that exist for a given field

multimedia_count_distinct_values_per_group()

Count the distinct number of field values that exist per the given field to group by

multimedia_download_query()

Dynamic download service: Query for multimedia objects and return result as a stream ...

multimedia_find()

Find a multimedia document by id

multimedia_find_by_ids()

Find multimedia document by ids

multimedia_get_distinct_values()

Get all different values that can be found for one field

multimedia_get_distinct_values_per_group()

Get all distinct values (and their document count) for the field given divided per distinct value of the field to group by

multimedia_get_field_info()

Returns extended information for each field of a multimedia document

multimedia_get_paths()

Returns the full path of all fields within a document

multimedia_get_setting()

Get the value of an NBA setting

multimedia_get_settings()

List all publicly available configuration settings for the NBA

multimedia_is_operator_allowed()

Checks if a given operator is allowed for a given field

multimedia_query()

Query for multimedia documents

geo_age()

Geological Age

geo_count()

Get the number of geo areas matching a given condition

geo_count_distinct_values()

Count the distinct number of values that exist for a given field

geo_count_distinct_values_per_group()

Count the distinct number of field values that exist per the given field to group by

geo_find()

Find a GEO area by id

geo_find_by_ids()

Find geo areas by ids

geo_get_distinct_values()

Get all different values that exist for a field

geo_get_distinct_values_per_group()

Get all distinct values (and their document count) for the field given divided per distinct value of the field to group by

geo_get_field_info()

Returns extended information for each field of a specimen document

geo_get_geo_json_for_locality()

Retrieve a GeoJson object for a given locality

geo_get_paths()

Returns the full path of all fields within a document

geo_get_setting()

Get the value of an NBA setting

geo_get_settings()

List all publicly available configuration settings for the NBA

geo_is_operator_allowed()

Checks if a given operator is allowed for a given field

geo_query()

Query for geo areas

metadata_get_allowed_date_formats()

Get allowed values for dates in queries

metadata_get_controlled_list_phase_or_stage()

Get allowed values for the field 'PhaseOrStage' in a specimen document

metadata_get_controlled_list_sex()

Get allowed values for the field 'Sex' in a specimen document

metadata_get_controlled_list_specimen_type_status()

Get allowed values for the field 'SpecimenTypeStatus' in a specimen document

metadata_get_controlled_list_taxonomic_status()

Get allowed values for the field 'TaxonomicStatus' in specimen and taxon documents

metadata_get_controlled_lists()

Get the names of fields for which a controlled vocabulary exists

metadata_get_rest_services()

List all available REST services and their parameters

metadata_get_setting()

Get the value of an NBA setting

metadata_get_settings()

List all publicly available configuration settings for the NBA

metadata_get_source_systems()

Get the data sources from which the data was retrieved

Clients

Clients classes to interact with the NBA

ApiClient

ApiClient class

SpecimenClient

Specimen operations

GeoClient

Geo operations

MultimediaClient

Multimedia operations

MetadataClient

Metadata operations

TaxonClient

Taxon operations

Utils

Convenience functions to interact with other packages

geo_age()

Geological Age

chronos_calib()

Make calibration table

Model

R6 Classes for complete NBA object model

Agent

Agent Class

AssociatedTaxon

AssociatedTaxon Class

BioStratigraphy

BioStratigraphy Class

ChronoStratigraphy

ChronoStratigraphy Class

Crs

Crs Class

DefaultClassification

DefaultClassification Class

Expert

Expert Class

Feature

Feature Class

FeatureCollection

FeatureCollection Class

Filter

Filter Class

GatheringEvent

GatheringEvent Class

GatheringSiteCoordinates

GatheringSiteCoordinates Class

GeoArea

GeoArea Class

GeoJsonObject

GeoJsonObject Class

GeometryCollection

GeometryCollection Class

GroupByScientificNameQuerySpec

GroupByScientificNameQuerySpec Class

Iptc4xmpExt

Iptc4xmpExt Class

LineString

LineString Class

LithoStratigraphy

LithoStratigraphy Class

LngLatAlt

LngLatAlt Class

Monomial

Monomial Class

MultiLineString

MultiLineString Class

MultiMediaContentIdentification

MultiMediaContentIdentification Class

MultiMediaGatheringEvent

MultiMediaGatheringEvent Class

MultiMediaObject

MultiMediaObject Class

MultiPoint

MultiPoint Class

MultiPolygon

MultiPolygon Class

NamedArea

NamedArea Class

Organization

Organization Class

Path

Path Class

Person

Person Class

Point

Point Class

Polygon

Polygon Class

QueryCondition

QueryCondition Class

QueryResult

QueryResult Class

QueryResultItem

QueryResultItem Class

QueryResultItemObject

QueryResultItemObject Class

QuerySpec

QuerySpec Class

Reference

Reference Class

Response

Response Class

RestService

RestService Class

ScientificName

ScientificName Class

ServiceAccessPoint

ServiceAccessPoint Class

SortField

SortField Class

SourceSystem

SourceSystem Class

Specimen

Specimen Class

SpecimenIdentification

SpecimenIdentification Class

SummaryScientificName

SummaryScientificName Class

SummarySourceSystem

SummarySourceSystem Class

SummaryVernacularName

SummaryVernacularName Class

Taxon

Taxon Class

TaxonDescription

TaxonDescription Class

TaxonomicEnrichment

TaxonomicEnrichment Class

VernacularName

VernacularName Class

Data

Test data

shark_tree

A molecular phylogeny of the sharks

Package

nbaR package

nbaR

nbaR : R Package Client for the Netherlands Biodiversity API